Comparative analysis of root trabscriptome reveals candidate genes and expression divergence of homeologs in response to drought stress in wheat

Crops with a larger root system have an increased ability to absorb water and nutrients under water deficit condition. To unravel the molecular mechanism of drought induced root growth response, we performed RNA-Seq analysis of two wheat genotypes, Colotana 296-52 (Col) and Tincurrin (Tin) with contrasting root growth, under PEG treatment for 6 h. A total of 3,692 differentially expressed genes (DEGs) were specifically upregulated in drought-tolerant Col under PEG exposure relative to control (CK) treatment. Functional enrichment analyses revealed that GO terms such as generation of precursor metabolites and energy, oxidative phosphorylation, oxidation reduction, and KEGG pathways including oxidative phosphorylation, metabolic pathways and glutathione metabolism were the highly enriched terms among upregulated DEGs in Col, which may mediate root growth mechanism. We observed that DEGs related to glycolysis, proline biosynthesis, ethylene production, auxin transport, several transcription factors (TFs) and stress protection enzymes were among upregulated DEGs in Col roots, which was in consistent with functional enrichment analyses. The variant calling between Col and Tin detected 15,207 SNPs and InDels, which may affect protein function and mediate contrasting root length phenotype between two genotypes. Finally, the expression patterns of five Triads containing at least one candidate gene in response to heat, cold and salt stresses were analyzed by using qRT-PCR. Relative mRNA abundance of the Triads varied considerably under different abiotic stresses. Most notably, the B-homeolog of Triad-38844 was upregulated under heat and cold stresses but it was downregulated under salt stress in both genotypes. Our results provide further evidence for the expression variation of genes duplicated in allopolyploids. Moreover, the variation of homoeologous gene expression in response to environmental stresses may enable plants to better cope with stresses in their natural environments.